UFO: Afterlight takes us to Mars, where a human colony has been built with the help of the Reticulans not long before the events of UFO: Aftershock took place.
The Martian base is self-sustainable and provides all the necessities for the survival of humans on a foreign planet, mainly breathable air, water and food. Although the people inhabiting this colony have the technologies and knowledge required for their further development, basic survival is their major concern. Their only activity is research of a nearby excavation site, which proves the existence of an ancient, intelligent and highly developed alien civilization.

The story is situated on Mars. It starts where UFO: Aftermath left off and runs simultaneously with UFO: Aftershock. While the Laputans on Earth are fighting Wargots and Starghosts and finding out what caused the destruction of their home planet, a small colony on Mars is trying to survive and flourish.
The player will gain more details about the activities of intergalactic organisms, called Myrmecols, in the solar system. The scientific research and communication with different factions on the Earth gives him a different perspective on the events of the two previous sequels. In UFO: Afterlight, the players will meet with brand new technologies, unusual environment and enemies both old and unknown.